UCI Genomics High-Throughput Facility
Facility Description
August 2015
The UCI Genomics High-Throughput Facility (GHTF) has been in operation since 1999 and currently offers
microarray and next generation DNA sequencing support for clients within and outside the University of
California system. The GHTF is a Shared Resource funded in part by the Chao Family NCI-Comprehensive
Cancer Center Support Grant (P30CA062203) from the National Cancer Institute. Depending on client needs,
the facility can prepare mRNA, small RNA, genomic, ChIP, methyl and exome sequencing libraries. GHTF staff
have experience with multiple strategy options for exome enrichment, ribosomal RNA depletion and generation
of multiplex libraries in order to insure maximal return of data from experiments.
i)
Instrumentation: The GHTF is equipped with a Covaris S2 focused sonicating shearer; Sage Sciences
Blue Pippin electrophoresis system for DNA sizing and protein fractionation, NanoDrop 1000
Spectrophotometer, Qubit fluorometer, MJ Research Tetrad thermalcycler, Agilent 2100 Bioanalyzer,
and Agilent MX PRO RTPCR to facilitate the preparation of libraries and quality testing and final
titration of samples. The Fluidigm C1 single cell autoprep system for capturing single cells and
preparing templates is available for single cell genomic applications. The Affymetrix microarray platform
is utilized for gene expression studies, and analyzing known DNA SNPs and CNVs. Sequencing is
currently performed using the Illumina HiSeq 2500 with a dual mode system for either high output or
rapid mode sequencing. For long reads, the GHTF offers Pac Bio RS II sequencing, a capability that is
useful for whole genome assembly, targeted sequencing and for studying base modifications. Digital
gene expression and miRNA analysis is performed on the NanoString through campus shared access.
ii)
Software and Bioinformatic Analysis: All sequence data from the GHTF are piped to the Institute for
Genomics and Bioinformatics (IGB) where they are analyzed using an Illumina pipeline or PacBio RS
software. The IGB is under the supervision of Professor Pierre Baldi (UC Irvine, Information and
Computer Sciences; Director, IGB). Data are reported to users as aligned or not aligned fastq files
depending on user specification. Several software programs including Genomics Workbench (CLC
Bio) and JMP Genomics (SAS) are installed in the GHTF for client data analysis. Clients of the GHTF
have access to the campus high performance computing (HPC) cluster for analysis of sequences
involving large amounts of data processing. The computer cluster is a shared computing cluster
supervised by a GridEngine scheduler and has ~2000 64 bit cores including 25 nodes of 64 cores with
an aggregate 8.8TB RAM and 500 TB storage in a Gluster distributed filesystem. Clients have priority
on four 512 GB computing nodes with shared access to the rest of the cluster via a “Free Queue”
system that gives users access to maximum computational power as it harnesses unused cycles
throughout the cluster regardless of ownership/assignment.
iii)
Staff: Dr. Suzanne Sandmeyer (Professor, Dept. of Biological Chemistry) is faculty director of the
GHTF, and Dr. Melanie Oakes (PhD, Dept. of Biological Chemistry) is the facility manager and provides
pre- and post-consult for GHTF users. In addition, GHTF bioinformaticist, Jenny Wu, Ph.D., supports
clients in post-pipeline analysis on a recharge basis. Consultation for planning experiments and for
grant writing in the areas of microarrays, next generation sequencing and bioinformatics and statistics
is available and encouraged.
iv)
Classes: The GHTF offers monthly/quarterly training classes and tutorials in using Linux and Open
Source software on the HPC cluster as well as Bioinformatics (in conjunction with HPC staff) and also
offers classes in BigData processing (with faculty in Information & Computer Sciences). The GHTF is
committed to bringing new technology platforms to the campus and regularly sponsors technology
seminars.